Audio quality is highly dependent upon both the quality and placement of the external microphone you are using. Plug in a good set of sound isolating headphones to adjust the placement and aiming of your external mic while doing a test recording. Typical consumer grade microphones will be very directional across part of their frequency range so although typically you should aim the typical microphone at the subject area of interest some experimentation is necessary especially with lower cost mics. A small change in location and microphone direction has a huge impact upon the "color" of the audio it provides and that is especially true in a building with mostly hard acoustic surfaces like a typical church.
If your church is using microphones and speakers to amplify the output from the organist/choir then you want to be sure that your mic is picking up primarily either the direct audio from the performers OR the output from the speakers but not both simultaneously in a near even amplitude mix or you will get odd phase cancellation of some of the tonal range. If the church is using an amplified system, then using a line output from their mixing console via an adjustable attenuator into your camera mic input will provide better audio than using a low cost external mic.
The manual specifies that the "audio scene" setting can be used to change the behavior of the internal microphone but it doesn't explicitly state that it won't impact the external mic. Try changing that setting to see whether it is also tailoring the audio when an external microphone is used. Your HF800 manual is like a lot of recent Canon manuals that attempt to be very user friendly and in the process don't provide sufficient data and information about functions/features.
Rodger
EOS 1DX M3, 1DX M2, 1DX, 5DS R, M6 Mark II, 1D M2, EOS 650 (film), many lenses, XF400 video
